Term clarification: mycelium development

[dianeoinglis]

GO:0043581 mycelium development PMID:12832397 Definition: The process whose specific outcome is the progression of the mycelium over time, from its formation to the mature structure. A mycelium consists of a mass of branching, thread-like hyphae.

This term and definition do not make sense. It's not clear what "mature structure" results from "the progression of the mycelium over time." The way this definition is worded, it better describes a mycelium that acquires "developmental competence" for sporulation than the process the reference describes which is "aerial mycelium formation,""aerial mycelium development" or "aerial hyphal growth." A filamentous fungus that cannot make aerial mycelia still grows as a mycelium but cannot overcome surface tension to extend its hyphae vertically and has a noticeably different colony appearance

PAMGO has made a lot of primary annotations to this term and likely just knows what it means when applied to the strictly filamentous fungal plant pathogens they annotate. If the term is inferred across other fungal species though, the term and its definition become confusing. I can contact PAMGO and clarify how they use the term and if the definition could be made more clear/specific across the broad range of fungal species. Is Ralph Dean the main contact at PAMGO?

Diane

[tberardini]

Hi Diane,

It looks like the 'standard' x development definition was applied when creating this term. We should certainly improve the definition or change the primary term name to better reflect its intended use. Yes, please contact PAMGO for clarification. I don't know who the main contact at PAMGO - Candace Collmer and Trudy Torto-Alalibo were the main persons working on this project. Perhaps try them first.

ccollmer@wells.edu trudy@vbi.vt.edu

[dianeoinglis]

Candace responded that she is retired and the email to Trudy failed. Candace suggested Brett Tyler be contacted and our PAMGO info updated. I just got an out of town until 8/26 autoresponse from Brett's email address. Brett.Tyler@oregonstate.edu.

[tberardini]

Time to follow up with Brett?

[dianeoinglis]

I emailed him and received out-of-office reply. I emailed him again about 2 days after the return date. I will email again shortly and include a cc to another contact mentioned in the o-o-o reply.

[tberardini]

Thanks for the update.

[dianeoinglis]

While I am waiting for a response from Brett Tyler or someone with PAMGO, I am going to request the specific term "aerial mycelium formation" and let them know that this term has been created and that I would like to request the ambiguous term "mycelium development" be obsoleted because it has another meaning in other fungal species. I will create a new ticket the NTR and re-send the email.

[tberardini]

Good idea, Diane! Is there another term (or maybe more than one additional term) that could be requested at the same time as 'aerial mycelium formation' that would cover other instances where 'mycelium development' has been used for annotation? If you can think of such a term or terms, then that will make reannotation easier for other curator. If you can't think of alternative terms, we'll wait for feedback to come back on the 'mycelium development' obsoletion proposal.

Thank you.

[dianeoinglis]

See NTR #12659 for aerial mycelium formation. Will also consider the other type and make that request as well.

[dianeoinglis]

An additional comment on "aerial mycelium formation" is that this is a pre-sporulation process and is also referred to as a "fertile mycelium." The term should probably have "asexual reproduction" as a parent. This process is not exclusive to fungi. The bacterium Streptomyces coelicolor and Streptomyces africanus sp.also do this before sporulating. The species that form an aerial mycelium develop conidiophores at the ends of the aerial hyphae.

The other type of "mycelium development" is also a pre-sporulation process but is called "developmental competence" in other fungi. This means that upon germination, an immuture mycelium formas and must grow for a period of time in order to become suffiently mature before the developmental process conidiophore formation and conidia develpment can occur. With "developmental competence" ther is no obvious change in the direction of growth. I think the term "developmental competence" is appropriate for the types of fungi that do not make aerial hyphae before they sporulate. The fungi that acquire developmental competence would grow continuously as vegetative hyphae/mycelia.

"Aerial mycelium development" should also get the synonym "aerial hyphal growth."

[dianeoinglis]

See #12660 for NTR: "mycelium reproductive competence"

[dianeoinglis]

Martin Urban from Phi-Base asks:" "Do you know if there is a way to obtain a list of all PAMGO terms that were already obsoleted from GO?"

[mah11]

As I recall, everyone was pretty conscientious about crediting the PAMGO term definitions to "GOC:pamgo_curators", so it should work to load GO into OBO-Edit and query for terms that have "any text field contains 'pamgo'" AND "has 'is_obsolete'".

[tberardini]

There are 117 terms that I get when I follow Midori's instructions.
(Sorry about the long list, I'll attach as a file instead.) obsoletedPAMGO.docx

[dianeoinglis]

Excellent. Thank you for the list.

There does not appear to be any objection to obsoleting the term "mycelium development" and replacing this ambiguous term with more specific terms. Another mycelium development term is is needed as well. I'm working on it. Martin Urban responded via contact@phi-base.org.. His specific email address for contact is martin.urban@rothamsted.ac.uk. Hi Diane, ‘Mycelium development’ can also occur within substrate (i.e. within an agar plate or wood). Could you help with a term for this as well? Martin

[tberardini]

@dianeoinglis : shall I send out an obsoletion alert for the current 'mycelium development' term then? http://amigo.geneontology.org/amigo/term/GO:0043581

[dianeoinglis]

Yes. The replacements are:

"aerial mycelium formation" substrate mycelium formation" "acquisition of mycelium reproductive competence"

[tberardini]

Summary: Replacement terms in these issues: "aerial mycelium formation" #12659, "(acquisition of ) mycelium reproductive competence"#12660, I can't find the one for 'substrate mycelium formation'. @paolaroncaglia , I will not send out the obsoletion email until the new terms have been added.

[martin2urban]

@tberardini: Hello, could you please let me know how you filtered the 117 obsoleted PAMGO terms? Just starting to learn Obo-edit 2 software. Beneath my attempt in a screenshot. Search for 'all_text_fields contains "pamgo" ' only gives 992 matches using go-basic.

Many thanks. martin.urban AT rothamsted.ac.uk

[dosumis]

That's a link filter/search. You need a term filter/search panel.

[paolaroncaglia]

Hi @tberardini , I added GO:0097736 'aerial mycelium formation' to start with.

[paolaroncaglia]

Hi again @tberardini , I also added GO:0097737 'acquisition of mycelium reproductive competence'. @dianeoinglis hasn't requested 'substrate mycelium formation' yet, but I think she will soon (see https://github.com/geneontology/go-ontology/issues/12659#issuecomment-253458272).

[paolaroncaglia]

Hi @tberardini , FYI, I just added GO:0097738 'substrate mycelium formation'.

[tberardini]

@dianeoinglis : were you able to sort out the filtering issue you had with OE? As David OS said, you should be using the term filter, not the link filter.

[tberardini]

Consider terms for 'mycelium development:

GO:0097736, aerial mycelium formation GO:0097738, substrate mycelium formation GO:0097737, acquisition of mycelium reproductive competence

I'll compose the obsoletion email and send it today.

[martin2urban]

@tberadini and @dosumis : I can now confirm that there are 117 obsoleted PAMGO terms when using the term filter. Many thanks!

[tberardini]

@fusarium : ok, great

[tberardini]

Sent today:

Dear all,

The proposal has been made to obsolete the following term:

GO:0043581 mycelium development

The reason for obsoletion is that the term is ambiguous. Three more clearly defined terms have been created that should be considered in its place:

GO:0097736, aerial mycelium formation GO:0097737, acquisition of mycelium reproductive competence GO:0097738, substrate mycelium formation

All details here:

https://github.com/geneontology/go-ontology/issues/12613

Experimental annotations to this term come from the PAMGO group and CGD.

We are opening a comment period for this proposed obsoletion. We'd like to proceed and obsolete the term above on November 1, 2016.

* Unless objections are received by November 1, 2016, we will assume that you agree to this change. *

On behalf of the GO ontology editors,

Tanya Berardini TAIR Curator www.arabidopsis.org

[tberardini]

Annotation counts (all): @fusarium and @dianeoinglis, these will need to be updated.

):

[tberardini]

Ontology edits are done.

[Term] id: GO:0043581 -name: mycelium development +name: obsolete mycelium development namespace: biological_process -def: "The process whose specific outcome is the progression of the mycelium over time, from its formation to the mature structure. A mycelium consists of a mass of branching, thread-like hyphae." [GOC:jl, ISBN:1580085792, PMID:12832397] -is_a: GO:0044767 ! single-organism developmental process -is_a: GO:0048856 ! anatomical structure development -intersection_of: GO:0048856 ! anatomical structure development -intersection_of: results_in_development_of FAO:0000011 ! mycelium -relationship: only_in_taxon NCBITaxon_Union:0000020 ! Fungi or Bacteria -relationship: part_of GO:0007275 ! multicellular organism development +def: "OBSOLETE. The process whose specific outcome is the progression of the mycelium over time, from its formation to the mature structure. A mycelium consists of a mass of branching, thread-like hyphae." [GOC:jl, ISBN:1580085792, PMID:12832397] +comment: The reason for obsoletion is that the term is ambiguous. Three more clearly defined terms have been created that should be considered in its place. +is_obsolete: true +consider: GO:0097736 +consider: GO:0097737 +consider: GO:0097738

[Term] id: GO:0043582 @@ -574595,7 +574594,8 @@ name: sclerotium development namespace: biological_process def: "The process whose specific outcome is the progression of the sclerotium over time, from its formation to the mature structure. A sclerotium is a mycelial resting body, resistant to adverse environmental conditions." [GOC:di, PMID:21148914] -is_a: GO:0043581 ! mycelium development +is_a: GO:0044767 ! single-organism developmental process +is_a: GO:0048856 ! anatomical structure development